GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvT in Shewanella sp. ANA-3

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate 7026359 Shewana3_3501 glycine cleavage system aminomethyltransferase T (RefSeq)

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__ANA3:7026359
          Length = 364

 Score =  508 bits (1307), Expect = e-148
 Identities = 246/361 (68%), Positives = 296/361 (81%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           MA +T L+ +H    A+MVDFHGW MPL+YGSQI+EHHAVR DAGMFDVSHMT+VD+ G+
Sbjct: 1   MANKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGT 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
               FLR LLANDVAKL   GKALY GML+ + G+IDDLI YY T+ F+R+VVNSATREK
Sbjct: 61  DACAFLRKLLANDVAKLKVPGKALYGGMLDDNAGIIDDLITYYLTDTFYRVVVNSATREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+WI + ++ F + +T R +L+MIAVQGPNA+AKAA +F+  Q  A+EGMKPFFG QAG
Sbjct: 121 DLAWIAKQSQGFDVTVTERPELAMIAVQGPNAKAKAAAVFSADQNAAIEGMKPFFGKQAG 180

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
            LFIATTGYTGE GYEI +P  +A   W+AL++ GVKPCGLGARDTLRLEAGMNLYG +M
Sbjct: 181 SLFIATTGYTGEVGYEIIVPETEAEALWQALLDQGVKPCGLGARDTLRLEAGMNLYGLDM 240

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRF 300
           DETI+PLAANMGWTIAWEP DRDFIGR+ALE  R+ GT+KLVGLVM EKGVLR+++PV F
Sbjct: 241 DETINPLAANMGWTIAWEPTDRDFIGRQALEALRDAGTDKLVGLVMEEKGVLRHDMPVFF 300

Query: 301 TDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNG 360
           TDA G + +G+ITSGTFSPTLGYSIA+ARVP  IG+TA V++R + + V+V  P FVRNG
Sbjct: 301 TDAAGVEQQGVITSGTFSPTLGYSIAMARVPNSIGDTAEVEMRKKRVAVRVVAPNFVRNG 360

Query: 361 K 361
           K
Sbjct: 361 K 361


Lambda     K      H
   0.320    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 486
Number of extensions: 12
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 7026359 Shewana3_3501 (glycine cleavage system aminomethyltransferase T (RefSeq))
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00528.hmm
# target sequence database:        /tmp/gapView.15192.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     3e-140  453.2   0.1   3.4e-140  453.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7026359  Shewana3_3501 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026359  Shewana3_3501 glycine cleavage system aminomethyltransferase T (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.0   0.1  3.4e-140  3.4e-140       2     362 .]       3     359 ..       2     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.0 bits;  conditional E-value: 3.4e-140
                         TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtk 78 
                                       ++t L++ h e  +k+vdf+Gw +P++y+s+ieeh+avr++aG+fDvshm+ v+++G+++ +fL++llanDv++L +
  lcl|FitnessBrowser__ANA3:7026359   3 NKTVLFNKHLESNAKMVDFHGWDMPLNYGSQIEEHHAVRQDAGMFDVSHMTVVDVTGTDACAFLRKLLANDVAKLKV 79 
                                       79*************************************************************************98 PP

                         TIGR00528  79 .GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGP....k 150
                                        Gka+y ++l  + G++DDli y+ ++  ++++vvn+at+ekDl+w+ ++ +++    t + e++++a+qGP    k
  lcl|FitnessBrowser__ANA3:7026359  80 pGKALYGGMLDDNAGIIDDLITYYLTDT-FYRVVVNSATREKDLAWIAKQSQGFDVTVTERPELAMIAVQGPnakaK 155
                                       8*************************99.*******************************************99999 PP

                         TIGR00528 151 aktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDt 227
                                       a++++   +++a+eg+k+ff+ q++ l     +ia+tGytGe G+ei+v++ +a  lw++l+++ gvkP+GLgarDt
  lcl|FitnessBrowser__ANA3:7026359 156 AAAVFSADQNAAIEGMKPFFGKQAGSL-----FIATTGYTGEVGYEIIVPETEAEALWQALLDQ-GVKPCGLGARDT 226
                                       999************************.....********************************.************ PP

                         TIGR00528 228 LrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvllt. 303
                                       Lrleagm+LyG ++de+i Pl+a++gw++++e++++dfiGr++le  ++ gt+k lvGl+m ekg++r++++v++t 
  lcl|FitnessBrowser__ANA3:7026359 227 LRLEAGMNLYGLDMDETINPLAANMGWTIAWEPTDRDFIGRQALEALRDAGTDK-LVGLVMEEKGVLRHDMPVFFTd 302
                                       ****************************************************99.*********************4 PP

                         TIGR00528 304 .ngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvrs 362
                                         g ++ G++tsGt+sPtLg++ia+a+v+   + iG+++eve+r+k v ++vv + fvr+
  lcl|FitnessBrowser__ANA3:7026359 303 aAGVEQQGVITSGTFSPTLGYSIAMARVP---NSIGDTAEVEMRKKRVAVRVVAPNFVRN 359
                                       446799***********************...99***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (364 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.82
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory